Category Archives: musing

Six manuscripts were published and an additional two were accepted and three more were submitted or being revised in 2016

Three graduate students survived another year in the lab: Sawyer, Nat, Derreck

Joined by one Microbiology graduate student Jesus Pena joined in Fall 2016.

Nine undergraduates worked in the lab Deane, Josh, Jericho, Dillon, Na, Justin, Serena, Leandra, George and Travis has been part of bioinformatics projects

One postdoc, Jinfeng has been the bioinformatics and genomics guru from genome assembly to transposon bioinformatics

One new assembly of a Citrus genome

At least 15 new genomes from our work with Zygolife and 1000 Fungal Genomes project were released or material processed. More than 100 cultures of some fungi are being examined in the lab.

One NSF grant started on systematics of anaerobic chytrid fungi and one new grant awarded as part of the UC MRPI http://ucop.edu/research-initiatives/programs/mrpi/2017-Awards.html program on the “UC Valley Fever Research Initiative” lead by UCSF and including several other UC campus.

Here’s our 2010 publications wordle made with pubmed2wordle using this query that includes paper co-authored by Jason, Divya, and John with this search. [h/t to Kevin’s blog for showing this easy app – had done this previously with a cmdline bioperl script]

Well the 1st quarter is over and had a few observations about life of an assistant professor.

Remember to check that you don’t need to turn in grades! I thought I could safely ignore emails about sending in grades, since I wasn’t teaching this quarter, but meant I forgot to turn in grades for grad students working in the lab. Whoops! Lesson learned.

Spending money isn’t that hard, but researching how to spend it on equipment is time consuming. The optimization of trying to find the best deal, planning for current and future experiments, and establishing new technologies took more time than I expected. Planning how to best spend money longer term is also taking some time, I don’t know if there is any good formula to rely on because it depends on what future grant support is awarded. But I think that I am getting better at making the equipment decisions – but I am my own sysadmin for macs in the lab and also the new separate (from the shared bioinformatics cluster) linux machines I have for our web and specialized compute needs and find that very time consuming.

Travel is good, but takes up time that can be spent writing, instructing, and my own research. While I can do much of my research from my laptop and an internet connect, I am distracted when away from lab and doing a disservice to the meeting I am attending if I am always working while on the road. Better to divide my time better and focus on the meeting at hand. Course this means I should always have the talks finished before I get to the meeting and that has been difficult to guarantee.

People are important. I can’t do all the research myself. Getting students and postdocs into the lab who can be trained on techniques and the background of the research questions is the most important thing to get the lab moving forward. I am excited about the teaching and learning process but it is a process that needs a vision and schedule that I establish. I’m still fine tuning that schedule and the approaches while keeping us aimed toward a vision of the kind of research we will do in the next 3-5 years.

Time flies – take stock of how you spent it! Stopping and reflecting on what was accomplished is good to remind me and remind trainees that we have done things even if it feels like there is a mountain of work ahead. As the gets better at this I’ll probably be able to give better feedback about dead-ends and keeping people on track earlier in the game. We are still getting our timing together to have regular lab meetings and journal clubs that I expect to be the heart of the learning that happens in the lab at this point. I’m teaching programming, bioinformatics, phylogenetics & molecular evolution, and mycology at the outset and so am working to make these subjects more approachable with the right kind of background reading materials. Probably will have to turn this into a review or primer someday as I feel like this synthesis of different fields is not something I can point anyone to just one or two resources for.

I’m still getting aquatinted with who to ask for help and where to go for advice, but I’ve been lucky to have generous junior and senior colleagues who have provided encouragement and advice. Here’s to hoping next quarter I learn a little more about how to do things, focus on the grant writing, and make some tangible progress on the research projects that need some new data before this summer. A lot of papers are queued up from collaborative work that were submitted this month and I hope that means more focus on the two main project foci of the lab. New folks will be joining us next quarter and I’m excited about the progress we have made and will be able to make as everyone comes up to speed.